[KevinH1990]

According to this web site: https://sites.google.com/site/mikefocke2/installinga%2703-%2704glasstopandframeona%2797

You can install an '03 or '04 glass windowed top on any of the earlier 986 Boxsters (1997-2002), which all came with a vinyl rear window from the factory. If you plan on installing one on a 1997 to 1999 Boxster, and want the more reliable operating system, then you will also have to replace the 'A Version' transmissions, mounting studs, cables, and double relay, as well as doing some rewiring in the areas briefly described above.

It looks like you can keep your “A version “ transmission, but the “B style” may be less trouble prone.